Pattern of early human-to-human transmission of Wuhan 2019-nCoV

Julien Riou; Christian L. Althaus

In a second step, we accounted for the uncertainty regarding the number of index cases n and the date T of the initial zoonotic animal-to-human transmissions at the wet market in Wuhan. An epidemic with several index cases can be considered as the sum of several independent epidemics with one index case each. We sampled (with replacement) n of the one-index-case epidemics, sampled a date of onset for each index case, and summed the epidemic curves together. The sampling of the date of onset was done uniformly from a two-week interval around November 27, 2019, in coherence with early phylogenetic analyses of 11 2019-nCoV genomes [7] . This step was repeated 4,800 times for each combination of R 0 (22 points) and k (20 points) for a total of 2,112,000 full epidemics simulated that included the uncertainty on D, n and T . Finally, we calculated the proportion of stochastic simulations that reached a total number of infected cases within the interval [1000, 9700] by January 18, 2020, as estimated by Imai and colleagues [8] . In a process related to Approximate Bayesian Computation (ABC), the parameter value combinations that led to simulations within that interval were treated as approximations to the posterior distributions of the parameters with uniform prior distributions. Model simulations and analyses were performed in the R software for statistical computing [9] . Code files are available on https://github.com/jriou/wcov.